Identifying changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting both nationally and subnationally in the United States of America. These results are impacted by changes in testing effort, increases and decreases in testing effort will increase and decrease reproduction number estimates respectively (see Methods for further explanation).
Using data available up to the: 2020-04-24
Note that it takes time for infection to cause symptoms, to get tested for SARS-CoV-2 infection, for a positive test to return and ultimately to enter the case data presented here. In other words, today’s case data are only informative of new infections about two weeks ago. This is reflected in the plots below, which are by date of infection.
Figure 1: The results of the latest reproduction number estimates (based on estimated confirmed cases with a date of infection on the 2020-04-13) in the United States of America, stratified by state, can be summarised by whether confirmed cases are likely increasing or decreasing. This represents the strength of the evidence that the reproduction number in each region is greater than or less than 1, respectively (see the methods for details). Regions with fewer than 40 confirmed cases reported on a single day are not included in the analysis (light grey).
| Estimate | |
|---|---|
| New confirmed cases by infection date | 27705 (27203 – 28214) |
| Expected change in daily cases | Decreasing |
| Effective reproduction no. | 1 (0.9 – 1) |
| Doubling time (days) | -180 (320 – Inf) |
| Adjusted R-squared | 0.07 (-0.17 – 0.28) |
Figure 2: A.) Confirmed cases by date of report (bars) and their estimated date of infection. B.) Time-varying estimate of the effective reproduction number. Light ribbon = 90% credible interval; dark ribbon = the 50% credible interval. Estimates are shown until the 2020-04-13.Dark grey ribbon = 50% credible interval. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence.
Figure 3: A.) Time-varying estimate of the rate of growth, B.) Time-varying estimate of the doubling time in days (note that when the rate of growth is negative the doubling time is assumed to be infinite), C.) The adjusted R-squared estimates indicating the goodness of fit of the exponential regression model (with values closer to 1 indicating a better fit). Estimates are shown until the 2020-04-13. Light ribbon = 90% credible interval; dark ribbon = the 50% credible interval. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence.
Figure 4: Confirmed cases with date of infection on the 2020-04-13 and the time-varying estimate of the effective reproduction number (light bar = 90% credible interval; dark bar = the 50% credible interval.). Regions are ordered by the number of expected daily confirmed cases and shaded based on the expected change in daily confirmed cases. The dotted line indicates the target value of 1 for the effective reproduction no. required for control and a single case required for elimination.
Figure 5: Time-varying estimate of the effective reproduction number (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in the regions expected to have the highest number of new confirmed cases. Estimates are shown up to the 2020-04-13. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The dotted line indicates the target value of 1 for the effective reproduction no. required for control.
Figure 6: Confirmed cases by date of report (bars) and their estimated date of infection (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in the regions expected to have the highest number of new confirmed cases. Estimates are shown up to the 2020-04-13. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence.
Figure 7: Time-varying estimate of the effective reproduction number (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in all regions. Estimates are shown up to the 2020-04-13. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence. The dotted line indicates the target value of 1 for the effective reproduction no. required for control.
Figure 8: Confirmed cases by date of report (bars) and their estimated date of infection (light ribbon = 90% credible interval; dark ribbon = the 50% credible interval) in all regions. Estimates are shown up to the 2020-04-13. Confidence in the estimated values is indicated by translucency with increased translucency corresponding to reduced confidence.
| State | New confirmed cases by infection date | Expected change in daily cases | Effective reproduction no. | Doubling time (days) |
|---|---|---|---|---|
| Alabama | 217 (171 – 263) | Unsure | 1 (0.9 – 1.2) | 600 (18 – Inf) |
| Arizona | 187 (149 – 226) | Unsure | 1 (0.8 – 1.1) | 210 (17 – Inf) |
| Arkansas | 155 (119 – 189) | Increasing | 1.5 (1.2 – 1.8) | 9.1 (5.5 – 26) |
| California | 1699 (1579 – 1827) | Increasing | 1.2 (1.1 – 1.3) | 18 (13 – 27) |
| Colorado | 366 (308 – 421) | Unsure | 1 (0.9 – 1.1) | 180 (22 – Inf) |
| Connecticut | 1202 (1100 – 1311) | Increasing | 1.2 (1.1 – 1.3) | 20 (14 – 39) |
| Delaware | 177 (138 – 221) | Likely increasing | 1.2 (1 – 1.4) | 22 (9.7 – Inf) |
| District of Columbia | 142 (106 – 178) | Unsure | 1.1 (0.9 – 1.3) | 38 (11 – Inf) |
| Florida | 707 (633 – 782) | Decreasing | 0.9 (0.8 – 0.9) | -25 (Inf – Inf) |
| Georgia | 736 (655 – 812) | Unsure | 1 (0.9 – 1) | -280 (36 – Inf) |
| Guam | 27 (10 – 41) | Unsure | 1 (0.5 – 1.5) | 32 (4.9 – Inf) |
| Idaho | 31 (12 – 48) | Unsure | 1 (0.6 – 1.5) | 43 (5.6 – Inf) |
| Illinois | 1503 (1397 – 1627) | Likely increasing | 1.1 (1 – 1.1) | 51 (26 – Inf) |
| Indiana | 451 (376 – 508) | Unsure | 1 (0.9 – 1.1) | 180 (23 – Inf) |
| Iowa | 302 (246 – 351) | Increasing | 1.4 (1.2 – 1.6) | 9 (6.3 – 16) |
| Kansas | 116 (83 – 143) | Likely increasing | 1.2 (1 – 1.5) | 14 (6.9 – 450) |
| Kentucky | 166 (127 – 201) | Likely increasing | 1.2 (1 – 1.3) | 21 (9.3 – Inf) |
| Louisiana | 427 (364 – 484) | Decreasing | 0.8 (0.7 – 1) | -35 (170 – Inf) |
| Maine | 19 (5 – 32) | Likely decreasing | 0.8 (0.4 – 1.1) | -7.6 (22 – Inf) |
| Maryland | 629 (559 – 712) | Unsure | 1 (0.9 – 1.1) | -400 (36 – Inf) |
| Massachusetts | 1672 (1553 – 1785) | Decreasing | 0.9 (0.9 – 1) | -73 (140 – Inf) |
| Michigan | 803 (713 – 881) | Decreasing | 0.9 (0.8 – 0.9) | -21 (Inf – Inf) |
| Minnesota | 128 (94 – 159) | Likely increasing | 1.1 (0.9 – 1.3) | 24 (9.2 – Inf) |
| Mississippi | 224 (183 – 268) | Unsure | 1.1 (0.9 – 1.2) | 54 (14 – Inf) |
| Missouri | 163 (126 – 202) | Likely decreasing | 0.9 (0.7 – 1) | -19 (220 – Inf) |
| Nebraska | 123 (86 – 152) | Increasing | 1.2 (1 – 1.5) | 15 (7.3 – Inf) |
| Nevada | 113 (79 – 142) | Unsure | 1 (0.8 – 1.1) | -76 (19 – Inf) |
| New Hampshire | 62 (38 – 84) | Unsure | 1.1 (0.8 – 1.3) | 110 (9.4 – Inf) |
| New Jersey | 3543 (3357 – 3721) | Likely increasing | 1 (1 – 1.1) | 130 (49 – Inf) |
| New Mexico | 105 (74 – 133) | Unsure | 1.1 (0.9 – 1.3) | 34 (9.8 – Inf) |
| New York | 5265 (5040 – 5493) | Decreasing | 0.8 (0.7 – 0.8) | -13 (Inf – Inf) |
| North Carolina | 269 (222 – 316) | Unsure | 1 (0.9 – 1.2) | 99 (17 – Inf) |
| North Dakota | 47 (22 – 66) | Likely increasing | 1.3 (0.9 – 1.8) | 11 (4.6 – Inf) |
| Ohio | 977 (883 – 1066) | Increasing | 1.3 (1.2 – 1.5) | 10 (7.6 – 16) |
| Oklahoma | 87 (60 – 113) | Unsure | 1 (0.7 – 1.2) | -54 (17 – Inf) |
| Oregon | 57 (31 – 75) | Unsure | 1 (0.7 – 1.3) | 1000 (10 – Inf) |
| Pennsylvania | 1293 (1185 – 1391) | Likely decreasing | 0.9 (0.9 – 1) | -110 (73 – Inf) |
| Puerto Rico | 60 (33 – 82) | Unsure | 1.1 (0.8 – 1.5) | 41 (7.5 – Inf) |
| Rhode Island | 343 (288 – 394) | Likely increasing | 1.1 (1 – 1.2) | 47 (16 – Inf) |
| South Carolina | 132 (99 – 169) | Likely decreasing | 0.9 (0.7 – 1.1) | -62 (20 – Inf) |
| South Dakota | 84 (57 – 109) | Likely decreasing | 0.8 (0.6 – 1) | -12 (Inf – Inf) |
| Tennessee | 263 (210 – 305) | Unsure | 1.1 (0.9 – 1.2) | 49 (15 – Inf) |
| Texas | 729 (643 – 797) | Decreasing | 0.9 (0.8 – 1) | -64 (78 – Inf) |
| Utah | 128 (88 – 157) | Unsure | 1.1 (0.9 – 1.3) | 26 (9.5 – Inf) |
| Vermont | 17 (0 – 33) | Unsure | 1.1 (0.3 – 1.8) | -18 (3 – Inf) |
| Virginia | 557 (490 – 627) | Increasing | 1.2 (1 – 1.3) | 21 (12 – 63) |
| Washington | 209 (165 – 252) | Unsure | 0.9 (0.8 – 1.1) | 160 (16 – Inf) |
| West Virginia | 38 (18 – 64) | Unsure | 1.1 (0.6 – 1.5) | 74 (6.5 – Inf) |
| Wisconsin | 162 (122 – 196) | Unsure | 1.1 (0.9 – 1.2) | 41 (12 – Inf) |
“2019 Novel Coronavirus Covid-19 (2019-nCoV) Data Repository.” 2020. Johns Hopkins CSSE. https://github.com/CSSEGISandData/COVID-19.
Abbott, Sam, Joel Hellewell, James D. Munday, and Sebastian Funk. 2020. “NCoVUtils: Utility Functions for the 2019-Ncov Outbreak.” - - (-): –. https://doi.org/10.5281/zenodo.3635417.
Xu, Bo, Bernardo Gutierrez, Sarah Hill, Samuel Scarpino, Alyssa Loskill, Jessie Wu, Kara Sewalk, et al. n.d. “Epidemiological Data from the nCoV-2019 Outbreak: Early Descriptions from Publicly Available Data.” http://virological.org/t/epidemiological-data-from-the-ncov-2019-outbreak-early-descriptions-from-publicly-available-data/337.
If you see mistakes or want to suggest changes, please create an issue on the source repository.
Text and figures are licensed under Creative Commons Attribution CC BY 4.0. Source code is available at https://github.com/epiforecasts/covid, unless otherwise noted. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".